SMTL ID : 9es9.1

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 13 residues within 4Å: Chain A: Q.47, G.51, M.54, R.83, H.86, R.87, A.90, F.131, G.135, L.138, P.139, H.187, T.188 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Q.47, A:A.90, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:T.188 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.2: 19 residues within 4Å: Chain A: Y.34, G.37, G.38, M.97, H.100, V.101, R.103, V.104, G.109, T.117, W.118, G.121, L.124, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.3 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.104, A:T.117, A:W.118, A:L.124, A:F.203 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.13: 13 residues within 4Å: Chain I: Q.47, G.51, M.54, R.83, H.86, R.87, A.90, F.131, G.135, L.138, P.139, H.187, T.188 13 PLIP interactions: 13 interactions with chain I, Hydrophobic interactions: I:Q.47, I:A.90, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:T.188 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.14: 19 residues within 4Å: Chain I: Y.34, G.37, G.38, M.97, H.100, V.101, R.103, V.104, G.109, T.117, W.118, G.121, L.124, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.15 15 PLIP interactions: 15 interactions with chain I, Hydrophobic interactions: I:V.101, I:V.104, I:T.117, I:W.118, I:L.124, I:F.203 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202

4 x HEC: HEME C(Covalent)

HEC.3: 11 residues within 4Å: Chain A: Y.34, C.35, G.38, T.42, R.207, G.210, I.211 Chain B: I.39, F.40, I.44 Ligands: HEM.2 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.39, B:F.40, B:I.44 Salt bridges: A:R.207 Metal complexes: H2O.1 HEC.8: 19 residues within 4Å: Chain C: Y.36, P.37, F.39, A.40, C.56, C.59, H.60, Q.94, L.104, N.105, V.106, G.107, A.108, N.188, G.190, R.191, G.192, I.194, P.196 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:Y.36, C:F.39, C:A.40, C:N.105, C:R.191 Hydrogen bonds: C:Q.94, C:N.105, C:Y.195 Salt bridges: C:R.191 pi-Stacking: C:F.39 Metal complexes: C:H.60 HEC.15: 11 residues within 4Å: Chain I: Y.34, C.35, G.38, T.42, R.207, G.210, I.211 Chain J: I.39, F.40, I.44 Ligands: HEM.14 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:I.39, J:I.44 Salt bridges: I:R.207 Metal complexes: H2O.5 HEC.20: 19 residues within 4Å: Chain K: Y.36, P.37, F.39, A.40, C.56, C.59, H.60, Q.94, L.104, N.105, V.106, G.107, A.108, N.188, G.190, R.191, G.192, I.194, P.196 11 PLIP interactions: 11 interactions with chain K, Hydrophobic interactions: K:Y.36, K:F.39, K:A.40, K:N.105, K:R.191 Hydrogen bonds: K:Q.94, K:N.105, K:Y.195 Salt bridges: K:R.191 pi-Stacking: K:F.39 Metal complexes: K:H.60

4 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.4: 8 residues within 4Å: Chain A: Q.15, A.18, D.19, T.22 Chain B: W.32 Chain C: N.319 Ligands: LMG.5, SQD.9 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:N.319, A:Q.15, A:D.19, A:T.22 Hydrophobic interactions: B:W.32, B:W.32 UMQ.12: 10 residues within 4Å: Chain A: M.92 Chain C: Q.72, A.73 Chain E: T.3 Chain G: F.5 Chain H: D.2, V.4, S.5, W.8, F.15 10 PLIP interactions: 4 interactions with chain H, 1 interactions with chain F, 4 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: H:F.15 Hydrogen bonds: H:D.2, H:S.5, C:Q.72, C:A.73, C:A.73, E:T.3 Water bridges: H:D.2, C:A.73 Salt bridges: F:R.101 UMQ.16: 8 residues within 4Å: Chain I: Q.15, A.18, D.19, T.22 Chain J: W.32 Chain K: N.319 Ligands: LMG.17, SQD.21 6 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J, 3 interactions with chain I Hydrogen bonds: K:N.319, I:Q.15, I:D.19, I:T.22 Hydrophobic interactions: J:W.32, J:W.32 UMQ.24: 10 residues within 4Å: Chain I: M.92 Chain K: Q.72, A.73 Chain M: T.3 Chain O: F.5 Chain P: D.2, V.4, S.5, W.8, F.15 10 PLIP interactions: 4 interactions with chain K, 4 interactions with chain P, 1 interactions with chain N, 1 interactions with chain M Hydrogen bonds: K:Q.72, K:A.73, K:A.73, P:D.2, P:S.5, M:T.3 Water bridges: K:A.73, P:D.2 Hydrophobic interactions: P:F.15 Salt bridges: N:R.101

2 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.5: 5 residues within 4Å: Chain A: Y.5, F.8, Q.15, I.17 Ligands: UMQ.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.8, A:I.17 Hydrogen bonds: A:Q.15 LMG.17: 5 residues within 4Å: Chain I: Y.5, F.8, Q.15, I.17 Ligands: UMQ.16 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:F.8, I:I.17 Hydrogen bonds: I:Q.15

2 x BNT: 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE(Non-covalent)

BNT.6: 7 residues within 4Å: Chain A: A.147, I.150, V.151 Chain B: I.75, P.77, F.85 Chain L: H.179 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.75, A:A.147 BNT.18: 7 residues within 4Å: Chain D: H.179 Chain I: A.147, I.150, V.151 Chain J: I.75, P.77, F.85 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.75, I:A.147

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.7: 13 residues within 4Å: Chain A: M.97, F.102, Y.105, G.125 Chain B: Y.80, P.83, V.84, M.101, P.105, L.108, F.133, G.136, V.139 9 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:V.84, B:P.105, B:L.108, B:F.133, B:V.139, A:F.102, A:Y.105 Water bridges: B:V.84 Metal complexes: H2O.2 CLA.19: 13 residues within 4Å: Chain I: M.97, F.102, Y.105, G.125 Chain J: Y.80, P.83, V.84, M.101, P.105, L.108, F.133, G.136, V.139 9 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.84, J:P.105, J:L.108, J:F.133, J:V.139, I:F.102, I:Y.105 Water bridges: J:V.84 Metal complexes: H2O.6

2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.9: 9 residues within 4Å: Chain B: W.32, L.45 Chain C: K.306, F.310 Chain D: R.66, N.70, L.73, L.77 Ligands: UMQ.4 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: B:L.45, D:L.77 Hydrogen bonds: B:W.32, D:N.70 Water bridges: B:Y.38, B:Y.38 Salt bridges: C:K.306, D:R.66 SQD.21: 9 residues within 4Å: Chain J: W.32, L.45 Chain K: K.306, F.310 Chain L: R.66, N.70, L.73, L.77 Ligands: UMQ.16 8 PLIP interactions: 3 interactions with chain L, 4 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: L:L.77, J:L.45 Hydrogen bonds: L:N.70, J:W.32 Salt bridges: L:R.66, K:K.306 Water bridges: J:Y.38, J:Y.38

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.10: 8 residues within 4Å: Chain D: C.158, H.160, L.161, G.162, C.163, C.176, H.179, S.181 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.158, D:H.160, D:C.176, D:H.179 FES.22: 8 residues within 4Å: Chain L: C.158, H.160, L.161, G.162, C.163, C.176, H.179, S.181 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.158, L:H.160, L:C.176, L:H.179

2 x BCR: BETA-CAROTENE(Non-covalent)

BCR.11: 10 residues within 4Å: Chain A: I.32, F.33, I.39, M.96 Chain F: T.110 Chain G: A.19, G.20 Chain H: F.15, L.19 Chain Q: L.39 9 PLIP interactions: 2 interactions with chain H, 4 interactions with chain A, 1 interactions with chain F, 1 interactions with chain G, 1 interactions with chain Q Hydrophobic interactions: H:F.15, H:L.19, A:I.32, A:F.33, A:F.33, A:I.39, F:T.110, G:A.19, Q:L.39 BCR.23: 10 residues within 4Å: Chain I: I.32, F.33, I.39, M.96 Chain N: T.110 Chain O: A.19, G.20 Chain P: F.15, L.19 Chain R: L.39 9 PLIP interactions: 4 interactions with chain I, 1 interactions with chain O, 1 interactions with chain R, 2 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: I:I.32, I:F.33, I:F.33, I:I.39, O:A.19, R:L.39, P:F.15, P:L.19, N:T.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pintscher, S. et al., Molecular basis of plastoquinone reduction in plant cytochrome b 6 f. Nat.Plants (2024)

Release Date

2024-10-16

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Cytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic: DL
Cytochrome b6-f complex subunit 6: EM
cytochrome b6-f complex subunit 7: FN
Cytochrome b6-f complex subunit 5: GO
Cytochrome b6-f complex subunit 8: HP
Thylakoid soluble phosphoprotein: QR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
I

B
B

J
J

C
C

K
K

D
D

L
L

E
E

M
M

F
F

N
N

G
G

O
O

H
H

P
P

Q
Q

R
R

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b6

Cytochrome b6-f complex subunit 4

Cytochrome f

Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

Cytochrome b6-f complex subunit 6

cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

Thylakoid soluble phosphoprotein

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